[gmx-users] nstlist and performances

[Riccardo Concu]

Dear all,
I'm running a simulation of a quite big system and is running very low
2ns/day. I need to boost-up the simulation speed but i don't know how. I
tried to use nstlist=10 but the system crash due to too many lincs
warning. Previously I minimized the system, then annealed and now i need
to run the production. All the statistics of the minimization step and
the anneling step seems good. Below I have attached the .mdp file.
Thank you,
Riccardo 

integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 2000000;4ns
comm-mode                = Linear
nstcomm                  = 10
comm-grps                = System
nstxout                  = 25000
nstvout                  = 25000
nstfout                  = 25000
nstlog                   = 25000
nstenergy                = 25000
nstxtcout                = 25000
xtc-precision            = 25000
xtc-grps                 = System
energygrps               = NAP NA WAT MET SI3 I LI+
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
periodic_molecules       = no
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
vdw-type                 = Cut-off
rvdw                     = 0.9
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 6
ewald_rtol               = 1e-5
optimize_fft             = yes
Tcoupl                   = v-rescale
tc-grps                  = System
tau_t                    =  0.1
ref_t                    = 298
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Isotropic
tau_p                    = 1
compressibility          = 4.5e-5
ref_p                    = 1.01325
gen_vel                  = yes
gen_temp                 = 298
gen_seed                 = 173529
constraints              = all-bonds
constraint-algorithm     = Lincs
lincs-order              = 4
lincs-iter               = 1